Publications

343 entries « 1 of 7 »

2023

Marin, Arnaldo; Mamun, Abdullah Al; Patel, Hima; Akamatsu, Hiroaki; Ye, Dan; Sudhan, Dhivya R; Eli, Lisa; Marcelain, Katherine; Brown, Benjamin P; Meiler, Jens; Arteaga, Carlos L; Hanker, Ariella B

Acquired secondary HER2 mutations enhance HER2/MAPK signaling and promote resistance to HER2 kinase inhibition in breast cancer Journal Article

In: Cancer Res, 2023, ISSN: 1538-7445.

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Schüß, Corinna; Vu, Oanh; Mishra, Nigam M; Tough, Iain R; Du, Yu; Stichel, Jan; Cox, Helen M; Weaver, C David; Meiler, Jens; Emmitte, Kyle A; Beck-Sickinger, Annette G

Structure-Activity Relationship Study of the High-Affinity Neuropeptide Y Receptor Positive Allosteric Modulator VU0506013 Journal Article

In: J Med Chem, vol. 66, no. 13, pp. 8745–8766, 2023, ISSN: 1520-4804.

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Junker, Hannes; Meiler, Jens; Schoeder, Clara T

Interplay of thermodynamics and evolution within the ternary ligand-GPCR-G protein complex Journal Article

In: Curr Opin Struct Biol, vol. 82, pp. 102656, 2023, ISSN: 1879-033X.

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Ledwitch, Kaitlyn V; Künze, Georg; McKinney, Jacob R; Okwei, Elleansar; Larochelle, Katherine; Pankewitz, Lisa; Ganguly, Soumya; Darling, Heather L; Coin, Irene; Meiler, Jens

Sparse pseudocontact shift NMR data obtained from a non-canonical amino acid-linked lanthanide tag improves integral membrane protein structure prediction Journal Article

In: J Biomol NMR, vol. 77, no. 3, pp. 69–82, 2023, ISSN: 1573-5001.

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McKee, Andrew G; McDonald, Eli F; Penn, Wesley D; Kuntz, Charles P; Noguera, Karen; Chamness, Laura M; Roushar, Francis J; Meiler, Jens; Oliver, Kathryn E; Plate, Lars; Schlebach, Jonathan P

General trends in the effects of VX-661 and VX-445 on the plasma membrane expression of clinical CFTR variants Journal Article

In: Cell Chem Biol, vol. 30, no. 6, pp. 632–642.e5, 2023, ISSN: 2451-9448.

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Gulsevin, Alican; Han, Bing; Porta, Jason C; Mchaourab, Hassane S; Meiler, Jens; Kenworthy, Anne K

Template-free prediction of a new monotopic membrane protein fold and assembly by AlphaFold2 Journal Article

In: Biophys J, vol. 122, no. 11, pp. 2041–2052, 2023, ISSN: 1542-0086.

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Woods, Hope; Schiano, Dominic L; Aguirre, Jonathan I; Ledwitch, Kaitlyn V; McDonald, Eli F; Voehler, Markus; Meiler, Jens; Schoeder, Clara T

Computational modeling and prediction of deletion mutants Journal Article

In: Structure, vol. 31, no. 6, pp. 713–723.e3, 2023, ISSN: 1878-4186.

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Selvasingh, Jazlyn A; McDonald, Eli Fritz; Mckinney, Jacob R; Meiler, Jens; Ledwitch, Kaitlyn V

Dark nanodiscs as a model membrane for evaluating membrane protein thermostability by differential scanning fluorimetry Miscellaneous

2023.

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Han, Bing; Gulsevin, Alican; Connolly, Sarah; Wang, Ting; Meyer, Brigitte; Porta, Jason; Tiwari, Ajit; Deng, Angie; Chang, Louise; Peskova, Yelena; Mchaourab, Hassane S; Karakas, Erkan; Ohi, Melanie D; Meiler, Jens; Kenworthy, Anne K

Structural analysis of the P132L disease mutation in caveolin-1 reveals its role in the assembly of oligomeric complexes Journal Article

In: J Biol Chem, vol. 299, no. 4, pp. 104574, 2023, ISSN: 1083-351X.

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Liessmann, Fabian; Künze, Georg; Meiler, Jens

Improving the Modeling of Extracellular Ligand Binding Pockets in RosettaGPCR for Conformational Selection Journal Article

In: Int J Mol Sci, vol. 24, no. 9, 2023, ISSN: 1422-0067.

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Liu, Yunchao Lance; Moretti, Rocco; Wang, Yu; Bodenheimer, Bobby; Derr, Tyler; Meiler, Jens

Integrating Expert Knowledge with Deep Learning Improves QSAR Models for CADD Modeling Miscellaneous

2023.

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Engdahl, Taylor B; Binshtein, Elad; Brocato, Rebecca L; Kuzmina, Natalia A; Principe, Lucia M; Kwilas, Steven A; Kim, Robert K; Chapman, Nathaniel S; Porter, Monique S; Guardado-Calvo, Pablo; Rey, Félix A; Handal, Laura S; Diaz, Summer M; Zagol-Ikapitte, Irene A; Tran, Minh H; McDonald, W Hayes; Meiler, Jens; Reidy, Joseph X; Trivette, Andrew; Bukreyev, Alexander; Hooper, Jay W; Crowe, James E

Antigenic mapping and functional characterization of human New World hantavirus neutralizing antibodies Journal Article

In: Elife, vol. 12, 2023, ISSN: 2050-084X.

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Marlow, Brennica; Kuenze, Georg; Meiler, Jens; Leman, Julia Koehler

Docking cholesterol to integral membrane proteins with Rosetta Journal Article

In: PLoS Comput Biol, vol. 19, no. 3, pp. e1010947, 2023, ISSN: 1553-7358.

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Okwei, Elleansar; Smith, Shannon T; Bender, Brian J; Allison, Brittany; Ganguly, Soumya; Geanes, Alexander; Zhang, Xuan; Ledwitch, Kaitlyn; Meiler, Jens

Rosetta's Predictive Ability for Low-Affinity Ligand Binding in Fragment-Based Drug Discovery Journal Article

In: Biochemistry, vol. 62, no. 3, pp. 700–709, 2023, ISSN: 1520-4995.

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Sala, Davide; Hildebrand, Peter W; Meiler, Jens

Biasing AlphaFold2 to predict GPCRs and kinases with user-defined functional or structural properties Journal Article

In: Front Mol Biosci, vol. 10, pp. 1121962, 2023, ISSN: 2296-889X.

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Martina, Cristina E; Crowe, James E; Meiler, Jens

Glycan masking in vaccine design: Targets, immunogens and applications Journal Article

In: Front Immunol, vol. 14, pp. 1126034, 2023, ISSN: 1664-3224.

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McDonald, Eli Fritz; Jones, Taylor; Plate, Lars; Meiler, Jens; Gulsevin, Alican

Benchmarking AlphaFold2 on peptide structure prediction Journal Article

In: Structure, vol. 31, no. 1, pp. 111–119.e2, 2023, ISSN: 1878-4186.

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2022

Fischer, Marion F S; Crowe, James E; Meiler, Jens

Computational epitope mapping of class I fusion proteins using low complexity supervised learning methods Journal Article

In: PLoS Comput Biol, vol. 18, no. 12, pp. e1010230, 2022, ISSN: 1553-7358.

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Mukherjee, Souhrid; Cassini, Thomas A; Hu, Ningning; Yang, Tao; Li, Bian; Shen, Wangzhen; Moth, Christopher W; Rinker, David C; Sheehan, Jonathan H; Cogan, Joy D; ; Newman, John H; Hamid, Rizwan; Macdonald, Robert L; Roden, Dan M; Meiler, Jens; Kuenze, Georg; Phillips, John A; Capra, John A

Personalized structural biology reveals the molecular mechanisms underlying heterogeneous epileptic phenotypes caused by KCNC2 variants Journal Article

In: HGG Adv, vol. 3, no. 4, pp. 100131, 2022, ISSN: 2666-2477.

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Nagel, Marcus; Moretti, Rocco; Paschke, Ralf; von Bergen, Martin; Meiler, Jens; Kalkhof, Stefan

Integrative model of the FSH receptor reveals the structural role of the flexible hinge region Journal Article

In: Structure, vol. 30, no. 10, pp. 1424–1431.e3, 2022, ISSN: 1878-4186.

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Alamo, Diego Del; Meiler, Jens; Mchaourab, Hassane S

Principles of Alternating Access in LeuT-fold Transporters: Commonalities and Divergences Journal Article

In: J Mol Biol, vol. 434, no. 19, pp. 167746, 2022, ISSN: 1089-8638.

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Choo, Charlene H; Chung, Doug D; Ledwitch, Kaitlyn V; Kassels, Alexa; Meiler, Jens; Aldave, Anthony J

Confirmation of association of p.Ser591Phe mutation with variant lattice corneal dystrophy Journal Article

In: Ophthalmic Genet, vol. 43, no. 4, pp. 530–533, 2022, ISSN: 1744-5094.

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Alamo, Diego Del; DeSousa, Lillian; Nair, Rahul M; Rahman, Suhaila; Meiler, Jens; Mchaourab, Hassane S

Integrated AlphaFold2 and DEER investigation of the conformational dynamics of a pH-dependent APC antiporter Journal Article

In: Proc Natl Acad Sci U S A, vol. 119, no. 34, pp. e2206129119, 2022, ISSN: 1091-6490.

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Roushar, Francis J; McKee, Andrew G; Kuntz, Charles P; Ortega, Joseph T; Penn, Wesley D; Woods, Hope; Chamness, Laura M; Most, Victoria; Meiler, Jens; Jastrzebska, Beata; Schlebach, Jonathan P

Molecular basis for variations in the sensitivity of pathogenic rhodopsin variants to 9-cis-retinal Journal Article

In: J Biol Chem, vol. 298, no. 8, pp. 102266, 2022, ISSN: 1083-351X.

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Aslanoglou, Despoina; Bertera, Suzanne; Friggeri, Laura; Sánchez-Soto, Marta; Lee, Jeongkyung; Xue, Xiangning; Logan, Ryan W; Lane, J Robert; Yechoor, Vijay K; McCormick, Peter J; Meiler, Jens; Free, R Benjamin; Sibley, David R; Bottino, Rita; Freyberg, Zachary

Dual pancreatic adrenergic and dopaminergic signaling as a therapeutic target of bromocriptine Journal Article

In: iScience, vol. 25, no. 8, pp. 104771, 2022, ISSN: 2589-0042.

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Sala, Davide; Alamo, Diego Del; Mchaourab, Hassane S; Meiler, Jens

Modeling of protein conformational changes with Rosetta guided by limited experimental data Journal Article

In: Structure, vol. 30, no. 8, pp. 1157–1168.e3, 2022, ISSN: 1878-4186.

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Blee, Alexandra M; Li, Bian; Pecen, Turner; Meiler, Jens; Nagel, Zachary D; Capra, John A; Chazin, Walter J

An Active Learning Framework Improves Tumor Variant Interpretation Journal Article

In: Cancer Res, vol. 82, no. 15, pp. 2704–2715, 2022, ISSN: 1538-7445.

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Brown, Benjamin P; Zhang, Yun-Kai; Kim, Soyeon; Finneran, Patrick; Yan, Yingjun; Du, Zhenfang; Kim, Jiyoon; Hartzler, Abigail Leigh; LeNoue-Newton, Michele L; Smith, Adam W; Meiler, Jens; Lovly, Christine M

Allele-specific activation, enzyme kinetics, and inhibitor sensitivities of EGFR exon 19 deletion mutations in lung cancer Journal Article

In: Proc Natl Acad Sci U S A, vol. 119, no. 30, pp. e2206588119, 2022, ISSN: 1091-6490.

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Kuntz, Charles P; Woods, Hope; McKee, Andrew G; Zelt, Nathan B; Mendenhall, Jeffrey L; Meiler, Jens; Schlebach, Jonathan P

Towards generalizable predictions for G protein-coupled receptor variant expression Journal Article

In: Biophys J, vol. 121, no. 14, pp. 2712–2720, 2022, ISSN: 1542-0086.

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Bozhanova, Nina G; Flyak, Andrew I; Brown, Benjamin P; Ruiz, Stormy E; Salas, Jordan; Rho, Semi; Bombardi, Robin G; Myers, Luke; Soto, Cinque; Bailey, Justin R; Crowe, James E; Bjorkman, Pamela J; Meiler, Jens

Computational identification of HCV neutralizing antibodies with a common HCDR3 disulfide bond motif in the antibody repertoires of infected individuals Journal Article

In: Nat Commun, vol. 13, no. 1, pp. 3178, 2022, ISSN: 2041-1723.

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Schäker-Hübner, Linda; Haschemi, Reza; Büch, Thomas; Kraft, Fabian B; Brumme, Birke; Schöler, Andrea; Jenke, Robert; Meiler, Jens; Aigner, Achim; Bendas, Gerd; Hansen, Finn K

Balancing Histone Deacetylase (HDAC) Inhibition and Drug-likeness: Biological and Physicochemical Evaluation of Class I Selective HDAC Inhibitors Journal Article

In: ChemMedChem, vol. 17, no. 9, pp. e202100755, 2022, ISSN: 1860-7187.

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Nebe, Michèle; Kehr, Stephanie; Schmitz, Samuel; Breitfeld, Jana; Lorenz, Judith; Duc, Diana Le; Stadler, Peter F; Meiler, Jens; Kiess, Wieland; Garten, Antje; Kirstein, Anna S

Small integral membrane protein 10 like 1 downregulation enhances differentiation of adipose progenitor cells Journal Article

In: Biochem Biophys Res Commun, vol. 604, pp. 57–62, 2022, ISSN: 1090-2104.

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Schoeder, Clara T; Gilchuk, Pavlo; Sangha, Amandeep K; Ledwitch, Kaitlyn V; Malherbe, Delphine C; Zhang, Xuan; Binshtein, Elad; Williamson, Lauren E; Martina, Cristina E; Dong, Jinhui; Armstrong, Erica; Sutton, Rachel; Nargi, Rachel; Rodriguez, Jessica; Kuzmina, Natalia; Fiala, Brooke; King, Neil P; Bukreyev, Alexander; Crowe, James E; Meiler, Jens

Epitope-focused immunogen design based on the ebolavirus glycoprotein HR2-MPER region Journal Article

In: PLoS Pathog, vol. 18, no. 5, pp. e1010518, 2022, ISSN: 1553-7374.

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Somermeyer, Louisa Gonzalez; Fleiss, Aubin; Mishin, Alexander S; Bozhanova, Nina G; Igolkina, Anna A; Meiler, Jens; Pujol, Maria-Elisenda Alaball; Putintseva, Ekaterina V; Sarkisyan, Karen S; Kondrashov, Fyodor A

Heterogeneity of the GFP fitness landscape and data-driven protein design Journal Article

In: Elife, vol. 11, 2022, ISSN: 2050-084X.

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Porta, Jason C; Han, Bing; Gulsevin, Alican; Chung, Jeong Min; Peskova, Yelena; Connolly, Sarah; Mchaourab, Hassane S; Meiler, Jens; Karakas, Erkan; Kenworthy, Anne K; Ohi, Melanie D

Molecular architecture of the human caveolin-1 complex Journal Article

In: Sci Adv, vol. 8, no. 19, pp. eabn7232, 2022, ISSN: 2375-2548.

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Zimmermann, Anne; Vu, Oanh; Brüser, Antje; Sliwoski, Gregory; Marnett, Lawrence J; Meiler, Jens; Schöneberg, Torsten

Mapping the Binding Sites of UDP and Prostaglandin E2 Glyceryl Ester in the Nucleotide Receptor P2Y Journal Article

In: ChemMedChem, vol. 17, no. 7, pp. e202100683, 2022, ISSN: 1860-7187.

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Phul, Saksham; Kuenze, Georg; Vanoye, Carlos G; Sanders, Charles R; George, Alfred L; Meiler, Jens

Predicting the functional impact of KCNQ1 variants with artificial neural networks Journal Article

In: PLoS Comput Biol, vol. 18, no. 4, pp. e1010038, 2022, ISSN: 1553-7358.

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Alamo, Diego Del; Sala, Davide; Mchaourab, Hassane S; Meiler, Jens

Sampling alternative conformational states of transporters and receptors with AlphaFold2 Journal Article

In: Elife, vol. 11, 2022, ISSN: 2050-084X.

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McDonald, Eli Fritz; Woods, Hope; Smith, Shannon T; Kim, Minsoo; Schoeder, Clara T; Plate, Lars; Meiler, Jens

Structural Comparative Modeling of Multi-Domain F508del CFTR Journal Article

In: Biomolecules, vol. 12, no. 3, 2022, ISSN: 2218-273X.

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Gulsevin, Alican; Glazer, Andrew M; Shields, Tiffany; Kroncke, Brett M; Roden, Dan M; Meiler, Jens

Veratridine Can Bind to a Site at the Mouth of the Channel Pore at Human Cardiac Sodium Channel Na1.5 Journal Article

In: Int J Mol Sci, vol. 23, no. 4, 2022, ISSN: 1422-0067.

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Borza, Corina M; Bolas, Gema; Zhang, Xiuqi; Monroe, Mary Beth Browning; Zhang, Ming-Zhi; Meiler, Jens; Skwark, Marcin J; Harris, Raymond C; Lapierre, Lynne A; Goldenring, James R; Hook, Magnus; Rivera, Jose; Brown, Kyle L; Leitinger, Birgit; Tyska, Matthew J; Moser, Markus; Böttcher, Ralph T; Zent, Roy; Pozzi, Ambra

The Collagen Receptor Discoidin Domain Receptor 1b Enhances Integrin β1-Mediated Cell Migration by Interacting With Talin and Promoting Rac1 Activation Journal Article

In: Front Cell Dev Biol, vol. 10, pp. 836797, 2022, ISSN: 2296-634X.

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Brown, Benjamin P; Vu, Oanh; Geanes, Alexander R; Kothiwale, Sandeepkumar; Butkiewicz, Mariusz; Lowe, Edward W; Mueller, Ralf; Pape, Richard; Mendenhall, Jeffrey; Meiler, Jens

Introduction to the BioChemical Library (BCL): An Application-Based Open-Source Toolkit for Integrated Cheminformatics and Machine Learning in Computer-Aided Drug Discovery Journal Article

In: Front Pharmacol, vol. 13, pp. 833099, 2022, ISSN: 1663-9812.

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Schmitz, Samuel; Schmitz, Emily A; Crowe, James E; Meiler, Jens

The human antibody sequence space and structural design of the V, J regions, and CDRH3 with Rosetta Journal Article

In: MAbs, vol. 14, no. 1, pp. 2068212, 2022, ISSN: 1942-0870.

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Bloodworth, Nathaniel; Barbaro, Natália Ruggeri; Moretti, Rocco; Harrison, David G; Meiler, Jens

Rosetta FlexPepDock to predict peptide-MHC binding: An approach for non-canonical amino acids Journal Article

In: PLoS One, vol. 17, no. 12, pp. e0275759, 2022, ISSN: 1932-6203.

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Maddur, Ashoka A; Voehler, Markus; Panizzi, Peter; Meiler, Jens; Bock, Paul E; Verhamme, Ingrid M

Mapping of the fibrinogen-binding site on the staphylocoagulase C-terminal repeat region Journal Article

In: J Biol Chem, vol. 298, no. 1, pp. 101493, 2022, ISSN: 1083-351X.

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Smith, Shannon T; Shub, Laura; Meiler, Jens

PlaceWaters: Real-time, explicit interface water sampling during Rosetta ligand docking Journal Article

In: PLoS One, vol. 17, no. 5, pp. e0269072, 2022, ISSN: 1932-6203.

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Rudolf, Sarina; Kaempf, Kerstin; Vu, Oanh; Meiler, Jens; Beck-Sickinger, Annette G; Coin, Irene

Binding of Natural Peptide Ligands to the Neuropeptide Y Receptor Journal Article

In: Angew Chem Int Ed Engl, vol. 61, no. 5, pp. e202108738, 2022, ISSN: 1521-3773.

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Tran, Minh H; Schoeder, Clara T; Schey, Kevin L; Meiler, Jens

Computational Structure Prediction for Antibody-Antigen Complexes From Hydrogen-Deuterium Exchange Mass Spectrometry: Challenges and Outlook Journal Article

In: Front Immunol, vol. 13, pp. 859964, 2022, ISSN: 1664-3224.

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2021

Bertron, Jeanette L; Duvernay, Matthew T; Mitchell, Sidnee G; Smith, Shannon T; Maeng, Jae G; Blobaum, Anna L; Davis, Dexter C; Meiler, Jens; Hamm, Heidi E; Lindsley, Craig W

Discovery and Optimization of a Novel Series of Competitive and Central Nervous System-Penetrant Protease-Activated Receptor 4 (PAR4) Inhibitors Journal Article

In: ACS Chem Neurosci, vol. 12, no. 24, pp. 4524–4534, 2021, ISSN: 1948-7193.

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McKee, Andrew G; Kuntz, Charles P; Ortega, Joseph T; Woods, Hope; Most, Victoria; Roushar, Francis J; Meiler, Jens; Jastrzebska, Beata; Schlebach, Jonathan P

Systematic profiling of temperature- and retinal-sensitive rhodopsin variants by deep mutational scanning Journal Article

In: J Biol Chem, vol. 297, no. 6, pp. 101359, 2021, ISSN: 1083-351X.

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343 entries « 1 of 7 »